Getting started
MERFISHEYES shows spatial transcriptomics data in 3D in your browser — cells, the molecules inside them, and the image underneath — and lets you share it.
From your files to a shared link
- 1Bring your dataRaw platform output (H5AD, Xenium, MERSCOPE, a transcripts file), an image, or data that is already processed.
- 2Load itPreview it in your browser, upload it to be processed on our servers, or open it from a public bucket.
- 3Explore itColour by gene or cell type, compare groups in plots, overlay molecules and an image, view two datasets side by side.
- 4Share itKeep it in your account, group it into projects, and submit it to the public Explore page.
Three kinds of data
Everything you load is one of three kinds. They are separate datasets, but they are shown together when they come from the same sample: molecules over the cells, the image under both.
| Cells | Molecules | Image | |
|---|---|---|---|
| What it is | One point per cell, with a gene expression matrix and cell metadata (cell types, clusters). | One point per detected transcript, labelled with its gene. | A microscopy image, such as a stitched DAPI mosaic. |
| Typical files | .h5adXeniumMERSCOPESpatialDataZarr | Parquet / CSVcolumn names | OME-Zarr (.zarr) |
| On the homepage | Single cell | Single molecule | Single cell → Folder |
Where to go next
| I have… / I want to… | Go to |
|---|---|
| Raw cells from a platform | H5ADXeniumMERSCOPEPreview itor process it on our servers |
| A transcripts file | Parquet / CSVcolumn namesthe single molecule viewer |
| An image | Image formatdrawing it under cells |
| Cells, molecules and an image of one sample | Upload them in one gooverlays in the viewer |
| Data that is already processed | How it opens as it isprocessed foldersSpatialDataZarr table |
| A dataset too big for my browser | Upload & process on serveror the Python scripts |
| Data on a public S3 bucket | Load from S3 |
| Not sure how to load it | Which way should I load my data?the three ways side by side |
| My own cell type labels | Cell types you assigned yourself |
| Find my way around the viewer | What is wherecolouring and plotstwo datasets side by side |
| Understand the expression values and DEGs | Where expression comes fromraw counts or loghow DEGs are calculated |
| Share what I am looking at | Links keep your view |
| Put my dataset on Explore | Step by stepwhat happens after I submitprojects |
Data formats →What you can bring, file by file.Loading data →Which way to load it, and what happens to it.Using the viewer →Colouring, plots, overlays, images and links.Expression & DEGs →Where values come from, raw vs log, and how DEGs are ranked.Sharing on Explore →Your account, projects, and getting reviewed.